Probabilistic base calling of Solexa sequencing data.

ABSTRACT:

Background

Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology.

Results

We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads.

Conclusion

We show

SUBMITTER: Rougemont J 

PROVIDER: S-EPMC2575221 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature